Ecology and Evolutionary Biology Commons^™

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Bugs, Birds, Blue: Queer Ecologies Of Embodiment, Kinship, And Survival, Celeste B. Newcomb

Theses and Dissertations

bugs, birds, blue is a multi-channel audiovisual installation that examines queer ecology as a framework for understanding transgender embodiment, kinship, and survival amid environmental crisis and ongoing political attacks on trans life (Mortimer-Sandilands and Erickson). Through sculpture, projection, sound, reflective surfaces, and biological imagery, the installation places human bodily matter alongside microbial and aquatic life forms to challenge narratives that frame trans existence as unnatural, recent, or isolated. Instead, the work proposes transness as relational, adaptive, and deeply entangled with broader ecological systems. The installation is composed of two interconnected environments. On one side of the space, three aquariums rest …

The Role Of Exotic Plants In The Diet Of Black-And-White Colobus Monkeys (Colobus Guereza) In Kibale National Park, Uganda, Michelle Gaykov

Theses and Dissertations

Exotic plants have both positive and negative impacts on their environment. They may act as additional food sources for the local fauna or as competition for local flora or leading to changes within a landscape or ecosystem. To considere the role of exotics in primate diet, this study focused on the dietary role of exotic plant species in the diet of a leaf-eating foregut fermenting monkey, the black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda. Int this study, I followed individuals in two groups of black-and-white colobus monkeys for 21 days recording their food intake (0700-1900). I also …

A Review Of Mockingbird Song, Jacqueline Milander

Student Theses

The northern mockingbird (Mimus polyglottos) is known for its large repertoire and highly versatile song patterns.  It is a frequent mimic that is thought to continue learning sounds from its environment for the duration of its life.  Utilizing available song studies, this is a comprehensive review of northern mockingbird song, including learning, mimicry, repertoires, song dependence on seasonal cyclicity, and song function, particularly interspecific territoriality. While much discussion has surrounded the idea that northern mockingbirds engage in interspecific territoriality and that vocal mimicry functions in intersexual selection, this review provides new insight into the possibility that latitudinal differences among populations …

Hidden In The Mist: Three New Species Of Salamanders Of The Genus Pseudoeurycea (Amphibia: Plethodontidae) From Oaxaca, Mexico, Eduardo A. Aguilar-Herrera, Salomón Sanabria-Urbán, Dulce L. Flores-Martínez, José David Gómez-Tapia, Misael Seba-Chacha, Leopoldo D. Vázquez-Reyes, Francisco A. Rivera-Ortíz, Patricia Ramírez-Bastida, Bruno Cortés-Ortiz, R. Alejandro Calzada-Arciniega, Etienne U. Avila-Ortega, Dónovan I. Víquez-Vega, Omar Hernández-Ordoñez, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

We describe three new species of lungless salamanders (Plethodontidae) in the genus Pseudoeurycea from Cerro Rabon, located on the eastern slopes of the Sierra Mazateca, Oaxaca, Mexico. This mid-elevation mountain, largely surrounded by warmer lowlands, remains relatively understudied. We present molecular and morphological evidence distinguishing the three new species from their congeners. According to our phylogenetic analysis, one of the new species belongs to the P. leprosa group, while the other two are members of the P. juarezi group. Notably, one of the new species represents the fourth worm salamander known from west of the Isthmus of Tehuantepec, and another …

Hybridization And Introgression In Marine Invertebrates: Population Genomics Of Phymactis Papillosa And Asterias Sea Stars, Christopher J. Dookie

Dissertations and Theses

Hybridization and introgression are evolutionary significant processes in marine invertebrates (Sanford & Kelly,2011) yet genome-wide investigations of gene flow in these taxa remain limited relative to vertebrate systems (Marchi et al., 2021). This thesis presents genomic analyses of hybridization and introgression in two marine invertebrates occupying contrasting oceanographic settings and characterized by contrasting genomic datasets: restriction-site associated DNA sequencing (RADseq) SNP data for the eastern Pacific sea anemone Phymactis papillosa and whole genome sequencing (WGS) data for the North Atlantic sea stars Asterias rubens and Asterias forbesi. For each system, I applied coalescent-based species tree inference using CASTER (Zhang …

Zero Textbook Cost Syllabus For Env 3070 (Agroecology), Benjamin Iuliano

Open Educational Resources

Our relationships with the food we eat are deeply personal, but also connect us to a wide array of people, plants, animals, and landscapes around the world. Encompassing a diversity of scholarly approaches, the field of agroecology seeks to understand the interactions among these components, draw attention to the consequences of our present industrial food system, and create the conditions for more sustainable and just futures. In this course, students will learn about the science, practice, and social movement of agroecology through lectures, course discussions, field trips, and hands-on activities.

The Evolution And Reproduction Of Andean Miconia (Melastomataceae), Juan Angulo

Dissertations, Theses, and Capstone Projects

Understanding the factors that shape diversification and distribution in tropical plant lineages is central to explaining the origins of Neotropical biodiversity. Assessing evolutionary history with trait evolution and climatic niche dynamics provides key insights into the drivers of diversification and biogeography, while natural history data remains critical for these evolutionary studies. The Tropical Andes, with its exceptional biodiversity and environmental heterogeneity, offers an ideal setting to explore these processes. In this dissertation, I investigate how reproductive systems, climatic niche dynamics, and pollination strategies influence the evolution and biogeography of Miconia III, a large and ecologically diverse clade in the …

Systematics, Biogeography, And Comparative Morphology Of Emerald And Tigertail Dragonflies (Anisoptera: Synthemistidae & Corduliidae), Aaron M. Goodman

Dissertations, Theses, and Capstone Projects

Dragonflies and damselflies (Odonata Fabricius, 1793) are among the most widely recognized and charismatic insect groups, whose significance have permeated throughout artwork, culture, and religion. They are highly mobile predators, currently consisting of ~ 6,500 species, and possessing some of the complex visual color systems, visual acuity, and flight patterns on Earth. Odonata are the among the earliest flying insects, with proto-odonates (Griffinflies) dating back to the Carboniferous (~360mya), with crown-odonata fossils stretching back to the Triassic (~250mya). Overall, dragonflies and damselflies are considered models of ecological and evolutionary research due to their long evolutionary history, range of habitats, and …

Origin And Maintenance Of The Andean Bird Fauna, Elkin A. Tenorio

Dissertations, Theses, and Capstone Projects

The origin and maintenance of the tropical montane diversity have been evaluated over multiple decades using various techniques and perspectives. Despite major progress in understanding phylogenetic relationships, diversification patterns, distributional data, and general ecology in the Andean biota, large gaps in our understanding remain, particularly in the synthesis across scales. To fill these gaps, I aimed to explore patterns and processes that underlie species diversification in birds of the tropical Andes of South America by combining different approaches using phenotypic, phylogenetic, and genomic data in multiple temporal and spatial scales.

In the first chapter, I examined the macroevolutionary patterns of …

Exploring The Role Of Ecological Traits In Shaping Spatial Patterns Of Genetic Diversity, Rilquer Mascarenhas Da Silva

Dissertations, Theses, and Capstone Projects

The field of comparative phylogeography aims at uncovering common underlying causes for shared patterns of diversity and diversification at the population level. However, it is now widely accepted that intraspecific genetic diversity patterns can differ considerably across co-occurring taxa due to ecological processes acting at the population level (and influencing individual movement and abundance). To model the processes underlying lineage diversification and demographic shifts in response to environmental changes, phylogeographers and population geneticists are now faced with the challenge of incorporating measurements of species ecological traits into their molecular studies. This dissertation aimed at investigating how different types of ecological …

Isolation And Divergence Of Greater Earless Lizards (Phrynosomatidae: Cophosaurus) In Western North America Support Multiple Diversification Processes And A Complex Demographic History, Christopher Robert Blair, Carlos Joaquín Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Thomas Panzera, Felipe De Medeiros Magalhães, Britt White, Uri Omar Garcia-Vazquez

Publications and Research

The Southwestern US and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (Cophosaurus texanus) to examine diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population …

Living Heritage, Resilience And Ethically Informed Infrastructures In Malawi, Martha B. Lerski, Frank Puluputu Mwale

Publications and Research

Rooted in a rural community’s needs, this paper explores how historically, and ethically informed infrastructures can support community engagement towards identification, documentation, and dissemination of local, traditional, and indigenous knowledge relating to climate change. The paper examines climate adaptation and sustainability issues through the lenses of community organizing and Library & Information Science best practices. It draws on a growing body of literature identifying a role for expanded epistemological and subject discipline perspectives. While the impacts of climate on material culture are increasingly recognized, intangible, and biocultural heritage have not received as much attention. Living heritage traditions and knowledge systems …

Disturbance And Diversity: Lichens In Changing Landscapes, Laura Boggess

Dissertations, Theses, and Capstone Projects

Disturbance is a fundamental ecological force that shapes biodiversity, community composition, and ecosystem function. Human-driven disturbances—such as habitat fragmentation, deforestation, and air pollution—are increasing worldwide, altering ecosystems at unprecedented rates. While ecological research has illuminated many effects of disturbance, significant knowledge gaps remain for underappreciated but ecologically vital organisms, such as lichens. Lichens are obligate symbioses between at least one fungus and one alga or cyanobacterium. As such, they are sensitive bioindicators of environmental change, offering unique insights into ecosystem health due to their responses to stressors such as poor air quality, habitat fragmentation, and deforestation. Yet, their responses to …

Individual, Social, And Environmental Factors Associated With Patterns Of Parasitic Infection In Capuchin Monkeys (Cebus Imitator), Megan C. Henriquez

Dissertations, Theses, and Capstone Projects

Parasites, and the infectious diseases they carry, are thought to have significantly impacted our evolutionary trajectory for millennia. Exploring how parasites are acquired and transmitted by their hosts in wild, natural populations is integral to understanding how similar processes may have shaped host-parasite co-evolutionary relationships over time. However, parasitological studies in humans and in non-human primates have produced inconsistent results, highlighting the dynamic, nuanced, and unique relationships individual parasites have with their hosts. These relationships are largely regulated by variation in factors at host, social, and environmental levels. Characteristics unique to the host (e.g., age and sex), factors pertaining to …

Decoding The Plant Metabolome: A Metabolomics Approach To Guereza (Colobus Guereza) Feeding Ecology In Kibale National Park, Uganda, Emma Grace Thurau

Dissertations, Theses, and Capstone Projects

Plant metabolites, an elusive and diverse group of plant chemicals, represent a complex chemical interplay between plants and herbivores. Plants contain essential nutrients necessary for herbivore survival, yet herbivore consumption results in negative fitness consequences to a plant. This relationship has triggered a coevolutionary arms race in which plants have evolved chemical defenses to prevent herbivore consumption and herbivores, in response, have evolved their own counter-adaptations. This arms race has led to the diverse numbers of herbivores and plants observed today; therefore, these plant metabolites act as a signature of evolution through their influence on herbivore adaptations. Plant metabolites are …

Phylogenetic Relationships And Species Delimitation Of Bunchgrass Lizards Of The Genus Sceloporus From Mexico With The Description Of A New Species, Tristan Charran, Jesús A. Loc-Barragan, Rafael Alejandro Calzada-Arciniega, Liz A. Alfaro-Juantorena, Raúl Cueva Del Castillo, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

Molecular data continue to serve as an invaluable tool to assess species limits and patterns of cryptic diversity, particularly in areas harboring high levels of biodiversity. The Sceloporus scalaris group, known as bunchgrass lizards, contains 13 described and one undescribed species distributed throughout high elevation biotas of Mexico. However, recent studies suggest that diversity in the group may be substantially underestimated. We collect new sequence data from four independent loci to determine the evolutionary distinctiveness and phylogenetic relationships of an isolated population of bunchgrass lizard in the Sierra San Juan (SSJ) in the Mexican state of Nayarit. Concatenation and coalescent-based …

Primates From Senèze, Eric Delson

Publications and Research

Senèze has yielded two primate fossils, neither from the recent field work. A partial ulna can be identified as cf. Macaca sylvanus. A nearly complete female skull is the holotype of Dolichopithecus arvernensis Depéret, 1928, now included in Paradolichopithecus. Emended and differential diagnoses are provided for this genus and species for the first time, and the Senèze skull is described and briefly compared to those of other species of the genus. Dental and cranial measurements are provided, along with comparative data. The macaque and Paradolichopithecus are moderately to highly terrestrial, respectively, and they suggest a woodland to more open …

Characterizing Malaria Infections In Caribbean Lizards: Parasite Niche Expansion & Host Response, Sarah J. Pangburn

Dissertations, Theses, and Capstone Projects

Malaria is historically one of the most severe parasitic human diseases and is still responsible for over half a million deaths annually. Plasmodium species, the causative agents of malaria, are often characterized by two hallmark features of their asexual stages: the invasion of vertebrate red blood cells and the presence of hemozoin pigment as a byproduct of host hemoglobin digestion. Despite their evolutionary relatedness to mammalian Plasmodium, wildlife malaria parasites are understudied, leaving their vast genetic diversity to be explored. Lizard-infective malaria parasites, for example, include over 100 species of Plasmodium and present a diverse array of phenotypes, some …

Quantified Lives: Data, Bias, And The Cost Of Categorization, Colin F. Geraghty

Dissertations, Theses, and Capstone Projects

This project critically examines how statistical methods and data visualization have historically been used to categorize, rank, and control human populations. By exploring the works of key figures like Francis Galton, Karl Pearson, and R.A. Fisher, it traces the evolution of categorization frameworks from their eugenic roots to modern applications in artificial intelligence and global metrics like the World Happiness Report. Through interactive visualizations and historical analysis, the project invites users to question the legitimacy of these frameworks and reflect on their impact on society. At its core, this work emphasizes the need to move beyond rigid classification systems, challenging …

Social Networks And Behavioral Adaptation Of Serrano Horses In A Rewilding Initiative In Spain, Ashley Bruno

Theses and Dissertations

Rewilding is a conservation measure that involves actively relocating species or restricting human land use to improve ecosystem sustainability. However, critics raise concerns that rewilding privileges ecosystem function over endangered species. Due to a lack of monitoring around species’ relocations, uncertainty lies in ecological outcomes and psychological, social, cultural impacts on affected animals. For this project, we collaborated with the non-profit Rewilding Europe that sought to conserve Serrano horses (Equus caballus), an ancient and under-studied breed of Spanish horse by relocating 11 individuals to a protected site in Guadalajara, Spain in June 2022. Our research aimed to address …

Karyotyping As A Method To Verify Phylogenetic Relationships Among The Enneacanthus Species, Ophelia A. Anderson

Theses and Dissertations

The Enneacanthus genus consists of three species of freshwater fish endemic to eastern North America: E. obesus (Banded Sunfish), E. gloriosus (Blue Spotted Sunfish), and E. chaetodon (Black Banded Sunfish). Previous studies using molecular data suggest that E. obesus and E. gloriosus are more closely related, with E. chaetodon as the most distantly related species in the genus. This study investigates the phylogenetic relationship among the Enneacanthus species, using karyotype characteristics - chromosome number, morphology and fundamental number - as comparative metrics. Chromosome spreads were obtained from scale and gill epithelium samples collected between 1993 and 1994. Prepared slides …

The Influence Of Environmental Change On Genetic Diversity Across Spatial And Taxonomic Scales, Connor M. French

Dissertations, Theses, and Capstone Projects

The spatial distribution of genetic diversity is of interest to biodiversity scientists and conservationists and is a fundamental metric of biodiversity. Genetic diversity patterns across spatial and taxonomic scales contain information about population and assemblage dynamics that can convey their resilience to environmental change. Ectotherms are especially linked to their environments and may be especially sensitive to fluctuations in the environment over time. Herein, I investigate global and regional patterns of genetic diversity in two groups of ectotherms, insects and lizards, to understand the relationship between environmental change and genetic diversity, from populations to assemblages. Overall, my research aims to …

Variability In Associations Among Seabirds And Marine Mammals: Causes And Consequences, Samantha A. Monier

Dissertations, Theses, and Capstone Projects

Marine predators today face multifaceted stressors from changing climate to changing prey availability, and these changes are occurring at unprecedented speeds. Any alteration to a species’ environment has the potential to disrupt social networks and thus, how animals obtain and transfer information. Interspecific social interactions in the form of local enhancement and facilitation are a critical, but not yet well-understood, component of seabird foraging; of immediate concern is that anthropogenic changes may be altering the quantity and quality of positive species interactions, with consequences for the species involved.

While we know these interactions are not immutable, less is known about …

The Effects Of Environmental Changes On The Biodiversity And Macroecological Patterns Of Bird Assemblages In The United States, Marlen Acosta Alamo

Dissertations, Theses, and Capstone Projects

The current restructuring of species assemblages and global loss of biodiversity result from species-specific responses to anthropogenic changes in climate and land cover. I investigated the effect of these two drivers on the seasonal distribution and biodiversity of birds in the United States and how human-induced habitat loss impacts macroecological patterns such as the species-area and the abundance-occupancy relationships. In Chapter 1, I examined the existence of a correlation between breeding and wintering geographic distributions of birds with different migratory strategies and the effect of changes in climate and the proportion of crop-pasture and urban land cover on this correlation. …

The Effects Of People, Time Of Day, And Season On Affiliative And Stereotypic Behaviors In Captive Rhinoptera Bonasus And Other Rays Across Two Human-Interactive Enclosures, Wren C. A. Newman

Theses and Dissertations

Cownose rays (Rhinoptera bonasus) are among the most common species found in aquaria, yet the impact of touch enclosures on their welfare remains largely unknown. While research on animal-visitor interactions has produced mixed results for other species, the lack of studies focusing on fish welfare poses a risk of overlooking potential welfare concerns. Therefore, we aimed to establish a baseline for cownose rays regarding stereotypic behaviors, sociality, and activity in captivity, and to examine the influence of human interaction on these behaviors. We collected over 700 hours of footage from two enclosures at Adventure Aquarium in Camden, NJ …

Listening For Lemurs: Translating Black-And-White Ruffed Lemur (Varecia Variegata) Vocalizations Into Conservation Insights Through Acoustic Monitoring, Carly H. Batist

Dissertations, Theses, and Capstone Projects

The field of bioacoustic monitoring has undergone a significant evolution in recent years, driven by technological innovations that have revolutionized how researchers study animal vocalizations. Traditionally, bioacoustics was rooted in active acoustic monitoring (AAM), involving human observers using recorders in the field to study animal sounds and understand species' vocal communication. However, the emergence of passive acoustic monitoring (PAM) has introduced a new complementary approach, utilizing specialized recorders placed in ecosystems to autonomously capture sounds at wide spatial and temporal scales. My dissertation adopts a translational approach to bioacoustic monitoring, integrating both AAM and PAM techniques to study and survey …

Systematics And Comparative Genomics Of The Petaluridae (Odonata: Anisoptera), Ethan R. Tolman

Dissertations, Theses, and Capstone Projects

The Anisoptera (Insecta: Odonata), or dragonflies exhibit diverse life histories and diversification patterns, with the family Petaluridae standing out as particularly unique. Comprising only 11 extant species, all of which inhabit increasingly threatened fen habitats, Petaluridae are known for their longevity, which can exceed five years, semi-terrestrial lifestyle, and remarkable physical size, ranking among the largest insects on Earth. Despite the evolutionary peculiarities of this family, no previous genomic studies have investigated the Petaluridae. This work presents two high-quality genome sequences and a targeted enrichment dataset to explore the chromosome architecture of Petaluridae, identifies genomic adaptations associated with their distinctive …

Using Leaf Spectra To Elucidate The Taxonomy And Ecology Of Living And Dried Plants, Natalia L. Quinteros Casaverde

Dissertations, Theses, and Capstone Projects

Identifying plants and understanding of changes in plant communities are crucial to the conservation and management of nature. The shortwave spectral reflectance of leaves is a promising tool for rapidly identifying species at different taxonomic ranks and predicting important plant functional traits. However, the spectral reflectance of leaves changes in response to biotic and abiotic conditions.

The aim of this dissertation is to investigate the potential of shortwave spectral reflectance to investigate (Chapter 1) how its variation affects the accuracy of methods used to predict plant taxonomies and what environmental factors most influence biophysically predicted traits, (Chapter 2) what are …

Adaptive Evolution Of Surface Proteins In Microbial Pathogens: Lyme Disease Pathogens (Borreliella Sp.) And Human Immunodeficiency Virus Type 1 (Hiv-1), Li Li

Dissertations, Theses, and Capstone Projects

Cell and virion surface proteins are key to the survival and adaptation of microbial pathogens by enabling them to evade host immune responses and to persist in diverse environments. Pathogens respond to host immune pressures with genetic changes in surface proteins through mechanisms including point mutations, recombination, gene duplication and loss, and lateral gene transfer, resulting in novel antigenic variants and antigenic diversity. This continuous adaptation helps pathogens evade host immunity, leading to chronic infections and recurrent disease outbreaks. Understanding these mechanisms is vital for developing effective strategies to combat infectious diseases.

This dissertation comprises three chapters exploring the adaptive …